An Over View of tics (6)

7/31/2019 An Over View of tics (6)

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An Over view of Bioinformatics

Bioinformatics: Application of it to thestorage, retrieval and analysis of

biological information, facilitated by theuse of computer.


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The central dogma of Bioinformatics

Sequence-Structure-Function

Evolution :In view-Invitro-Insilico The process of evolution has produced DNA

sequences that encode proteins with very

specific functions.


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Good Bioinformatician

Biological Language

Chemistry

Computational principles


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Components of Bio information

Sequence Analysis/Genomics

Structural Biology/Proteomics

Chemo informatics/Drug Designing Biocomputing


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Database Management

Databases are created to store, retrieve and

analyze the Biological data across the globe.

Databases:

Primary Databases: NCBI, EMBL, DDBJ

Secondary Databases: PDB, Sequence DB,

Structural DB, Motif DB, Genome DB,Proteome DB.


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Accession no, g i-Gene id

NCBI www.ncbi.nlm.nih.gov/Gene bank

EMBL www.ebi.ac.ac.uk/embl/ebi

DDBJ www.ddbj.nig.ac.jp Unigene

www.ncbi.nlm.nih.gov/unigene/tissue

information SCD database

www.staford.edu/Saccharomyces/yeast
http://www.ncbi.nlm.nih.gov/Genehttp://www.ebi.ac.ac.uk/embl/ebihttp://www.ddbj.nig.ac.jp/http://www.ncbi.nlm.nih.gov/unigene/tissuehttp://www.ncbi.nlm.nih.gov/unigene/tissuehttp://www.ddbj.nig.ac.jp/http://www.ebi.ac.ac.uk/embl/ebihttp://www.ncbi.nlm.nih.gov/Gene


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NCBI TOOLS

ORF-Open reading frame(select largest exon)

Map viewer- Select organism(gene name)

Vec Screen- Unwanted, contaminatednucleotides)

Electronic PCR- Primers, forward PCR, Reverse

PCR Human genome resource- Compares only

humans


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Bioedit (Offline tool) Primary analysis of protein:Nucleotide sequence, graphic representation,complementary sequence, reverse

complementary, RNA sequence, transcription,restriction mapping

BLAST

The nucleotide sequence is generated in fasta

format. Distribution of 158Blast hits on the query

sequence has been is seen


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Phylogenetic Analysis

Inthelastfewdecades,advancesinmolecular

biology and the equipment available for

research in this field have allowed the rapid

sequencing of genomes of several species

Computational Biology involves phylogenic

trees to examine evolutionary relations


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Tools:Offline

Pdraw: Rooted tree. Unrooted tree, Radial tree

Phylodraw :Root distance, Pair distance

It is used to see root distance.

It gives Unrooted tree, rooted tree and radialtree.

In Phylogram the distance between relatedspecies is seen.

In cladogram branching is seen.


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Clustal X :Multiple sequence alignment

Online

Clustal w : Multiple sequence alignment


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Primer 3 (On line) Submit nucleotide

sequence . It gives primers.


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Proteomics

Gen Scan (On line)Paste nucleotide

sequence- It gives protein sequence (peptides)

Gene Mark (Online)- Paste nucleotide

sequence-It gives protein sequence(Viruses)


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Protein Databases

Primary Structural database

Swiss-Prot

Secondary Structural databases

and TrEMBL and PIR

www.expasy.org

Primary structural analysis

Prot param

Prot scale
http://www.expasy.org/http://www.expasy.org/


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Secondary structural analysis

Tr EMBL, prosite ,Pfam

Tools GOR,SOPMA

Tertiary structural analysis

PDB,SCOP,CATH


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Visualization of protein

Tools

RASMOL

Cn3D Argus Lab

HEX


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Post Translational Modification

Signal P : peptide that binds to the protein

which help to cross the nuclear membrane-

can delete the signal peptides.

Sulfonators : Only thyrosine molecule can take

sulfonate

Net Acetyl : Acetylation of proteins

Net O Glyc : Glycoprotein

Net n Glyc : n Glycosylic bonds


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Active site prediction

Heteroatom

Cavity

Q-site finder: Q site Finder gives the activesites for the protein molecule.


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Energy Minimization

It is done for the stability of protein.

The protein structure of the virus that has

been stabilized will be used for drug design.

Tools

Spdbv, Argus Lab, Hex


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Drug Databases

Drug Bank: We have drug database has DrugBank from where we can find the suitabledrug and go for further modification

Ligand Info: Ligand Info system is based on theassumption that small molecules with similarstructure have similar functional properties.

The developed system enables a fast andsensitive index based search for similarcompounds in large databases.


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Tools used to design a drug

Chem draw tool can be used to draw the drug

molecule accordingly.

Hyperchem is used for proper geometric

optimization.

After the ligand is designed it has to go for

QSAR Properties.

Argus Lab is used for molecular modeling,

graphics and drug designing


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Conclusion

Using all these tools a novel drug for a foreign

protein can be designed.


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Drug Design

Tools: Free

Hyperchem-Docking

Argus Lab-Docking Licensed

CACHE-Construction of molecule

VEGA-Molecular Modeling


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An Over View of tics (6)